d1ur3m_d1k87a1

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1ur3_Mh	d1ur3m_	M215-M255,M263-M297	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	NAD(P)-linked oxidoreductase	Aldo-keto reductases (NADP)	Hypothetical oxidoreductase YdhF
1k87_Ac	d1k87a1	A138-A199,A200-A261	All alpha proteins	N-terminal domain of bifunctional PutA protein	N-terminal domain of bifunctional PutA protein	N-terminal domain of bifunctional PutA protein	N-terminal domain of bifunctional PutA protein

Justification for analogy
The motif in 1ur3: helix 1 and 4 are insertions while helix 2 and 3 are TIM barrel helices. So this is a hybrid motif.

In the alignments below, two upper-case letters are aligned, while two lower-case letters are NOT aligned. The two sequences in an alignment are NOT continuous in most cases (see their ranges). The superpositions are re-constructed from the corresponding alignments by minimizing the overall RMSD. In a PDB-format superposition file, the first domain is represented by chain S and the second domain is represented by chain A.

MANUAL alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1ur3_Mh   grlfnddYFQPLRDELAVVAEELNAgSIEQVVNAWVLRLPs---------------------------------------sgkieRVRAAVE-AETLk------mTRQQWFRIRKAALGydv-
1k87_Ac   -----qkNASGRAGMVQGLLQEFSL-SSQEGVALMCLAEAllripdkatrdalirdkisngnrspslfvnaatwgllftg-----NEASLSRsLNRIigksgeplIRKGVDMAMRLMGEqfvt

DALI alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1ur3_Mh   grlfnDDYFQPLRDELAVVAEELNAGSiEQVVNAWVLR--LPS-------------------S--------------gkiERVRAAVEAETLK------MTRQQWFRIRKAALGY-dv
1k87_Ac   -----QKNASGRAGMVQGLLQEFSLSS-QEGVALMCLAeaLLRipdkatrdalirdkisngnRspslfvnaatwgllftgNEASLSRSLNRIIgksgepLIRKGVDMAMRLMGEQfvt

TM alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1ur3_Mh   --------------GRL--FNDD-YFQPLRDELAVVAEEL-N---AGSIEQVVNAWVLRLPSSGKIERVRAAVEA----ETLKMTRQQWFRI------------RK-AAL--------------------------------GYDV
1k87_Ac   QKNASGRAGMVQGL--LQEFSLSSQEGVALMCLAEALLRIPDKATRDA-LI-------------------RDKISNGNR------S--PSLFVNAATWGLLFTGNEASLSRSLNRIIGKSGEPLIRKGVDMAMRLMGEQFVT----

FAST alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1ur3_Mh   GRLFNDDYF----QPLRDELAVVAEELNAGSIEQVVNAWVLRLPSSGK-------------------------------------------IERVRAAVEAETLKMT-----RQQWFRIRKAALGYDV---------
1k87_Ac   ---------QKNASGRAGMVQGLLQEFSLS-SQEGVALMCLAE-----ALLRIPDKATRDALIRDKISNGNRSPSLFVNAATWGLLFTGNEASLSRSLNRI------IGKSGEPLIRKGVDMAM----RLMGEQFVT